Hi Craig,
I don't work for or attend Stanford.
The signal comes over the air to an aerial antenna. If there were a connection issue between Puffers receiving antenna and the equipment that is encoding the signal it would affect all the channels and not just one channel.
There could be external interference between the tower that is broadcasting KGOs signal and Standord that could be causing poor, intermittent or no reception.
I'm pretty sure that driving around with frequency analyzers and troubleshooting the issue is beyond the scope of their research project and their research budget.
-Dean